<<apologies for duplicate - I hit 'send' by mistake''>>
Dear all,
I have a large number of homology models to produce which have ~90 - 95% homology with 10 high quality crystal structure templates.
Once I create my models I will be using GROMACS to relax the structure before comparing various properties of the models.
I wonder, is it a reasonable approach to energy minimize the templates and use these as templates for producing models thereby reducing the need for energy minimization on (a much larger number of) models?
Your opinion would be appreciated.
Best wishes, Dermot
On 12/19/2013 10:14 AM, Dermot Mallon wrote: > I wonder, is it a reasonable approach to energy minimize the templates > and use these as templates for producing models thereby reducing the > need for energy minimization on (a much larger number of) models?
I guess your assumption here is that if the input is GROMACS-relaxed, the output will be too. I doubt that will actually be the case, since the Modeller forcefield is different from the GROMACS one. I wouldn't touch the templates.
Ben Webb, Modeller Caretaker
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Dermot Mallon -
Modeller Caretaker